ISACB eCirculator Interview: Sasha Singh

Title: Director of Proteomics Research at the Center for Interdisciplinary Cardiovascular (CICS) Sciences at Brigham and Women’s Hospital (BWH)

Describe your research in a tweet (< 140 characters):

We make ideas fly by integrating innovative #proteomics workflows into the basic and clinical research of our collaborators #MassSpectrometry

How does your work fit in the context of applied cardiovascular biology?

As the ‘building blocks of the cell’ most research labs rely on a variety of biochemistry technologies to study their proteins of interest, however few have access to arguably the most advanced of these technologies, mass spectrometry. This limitation is not unique to applied cardiovascular biology but CICS/BWH leadership, namely Masanori Aikawa CICS’s founding director, recognized the need to have all-access to this technology. In 2012 I joined CICS as the Director of Proteomics Research and established a mass spectrometry group that collaborates very closely with the other directors that are specialists in various sub-disciplines of cardiovascular biology.

Pictured Left:Sasha (lowest head) directs the proteomics team at the Center for Interdisciplinary Cardiovascular Sciences.

CICS aims to expedite the bench-to-bedside transfer of new anti-coronary heart disease therapies or drug targets to the clinic. We are a collaboration between BWH and Kowa Scientific, a Japanese pharmaceutical company. By working together in a shared space, we anticipate a faster than usual turnaround of new therapies for the clinic.

Since most drug targets are proteins, mass spectrometry-enabled proteomics is essential to our goals. The most efficient way to identify candidate drug targets is through global proteomics screens. My lab is equipped with two mass spectrometers, and all necessary accessory equipment and reagents to perform both label (stable isotopes) and label-free global proteomics in any cell or tissue type. We are also involved in the data analysis portion of the screens; we use both conventional and custom software to screen through thousands of proteins to narrow down the list to a dozen or so leads that the biologists pursue further.

We also provide targeted proteomics support for proteins that are already under consideration as drug targets but require additional in vitro or in vivo validation experiments. In this case, we can design highly specific mass spectrometric methods that allow the biologist to enrich their target protein from the thousands of other proteins in their samples.

What is your relationship with ISACB?

I was introduced to ISACB through my collaboration with its President, Elena Aikawa. She is the Director of the Vascular Biology program at CICS and is not only my collaborator but one of my mentors. Elena is very forward-thinking and is a very strong supporter of mass spectrometry-guided research. As a consequence of her leadership role at ISACB and her drive to promote the benefits mass spectrometry and proteomics to cardiovascular biology research, she encouraged me to attend the ISACB meetings and webinars, and to get involved in this society. In fact, I will run a proteomics webinar in this Spring.

What is a routine day in your lab?

I usually skip into my office by 8:00 AM, take a sip of my coffee and then check my to-do list. Once a week I meet with each of my researchers: Hideyuki Higashi, a visiting scientist from Kowa and the main operator of the mass spectrometers, and Lang Ho Lee, my postdoctoral fellow (BWH) who is a bioinformatician.

At the beginning of each meeting we consult my writable (dry erase) wall where I have mapped out all of our collaborations, their goals, our contributions, and their statuses. The wall is very important to keep us oriented because we are extremely busy. One of our goals is to keep on track with all project timelines.

Usually, Hideyuki and I discuss trying new mass spectrometry methods to integrate into our collaborators’ projects. Hideyuki always returns the next week with a successful result. Lang Ho and I discuss in detail the specific and open-ended questions our collaborators wish to address in their data. Lang Ho always leaves the meeting excited about the challenge and returns as excited about his findings.

Pictured Below:Sasha uses two mass spectrometers to identify new drug targets at the Center for Interdisciplinary Cardiovascular Sciences at Brigham and Women’s Hospital.

At some point in the day, I skip into the lab to find out how the instruments are doing. Most of the times, they are running well. On some occasions, however, we do have technical issues but Hideyuki and I troubleshoot together to fix the problem. We seldom have downtime though. We have such high demand for instrument time that we perform preventive maintenance weekly to avoid issues. However, downtime is inevitable. Mass spectrometers and their accessory equipment are robust but also comprise some delicate parts that can get damaged from time-to-time.

If I am not chatting with my researchers, I am meeting with one of the CICS postdoctoral fellows that are running a proteomics experiment. The fellows understand that it isn’t enough to submit samples and get back pages of protein data. They want to learn more about the technology and how their specific mass spectrometric experiments impact their results. My group therefore spends a lot of time with the fellows to teach them about mass spectrometry, proteomics, and data analysis. The fellows usually enjoy learning about the technology, and its strengths and weaknesses. It enables them to make the wisest decisions for their data analysis and for the design of their next experiment.

Some days I am busy editing or writing a manuscript, or doing artwork for papers. I often get asked to draw figures for the other directors at CICS.

Overall, a routine day is a lot of fun in my lab. There is always an exciting development to hear about. I think that is why I skip a lot.

What led you to research in proteomics and mass spectrometry?

In 2007 I was recruited from Toronto to Boston to join the mass spectrometry labs of Judith and Hanno Steen at Boston Children’s Hospital. At that time, they were looking for researchers with a strong molecular and cell biology background to further expand their mass spectrometry capabilities and applications. My background was already divers, genetics, developmental biology and protein crystallography, but I had limited knowledge of mass spectrometry. Once I began working with the Steens, however, I was completely motivated to learn more about the technology. At some point, I realized that I could never do research again unless I could have access to mass spectrometers. It looks as though I will not have to worry about that.

What is coming in the future in proteomics and mass spectrometry?

That is a great question. For the instrumentation, no doubt, faster, more sensitive and more accurate/precise technology is always in the future. The instruments will continue to be more complex under the hood, but the user interfaces will improve in parallel allowing non-expert users to run sophisticated experiments with greater ease. My favorite development is in high resolution/accuracy mass (HRAM) spectrometers. HRAM technology allows us to see more information in our proteomics data and with more confidence than ever before.

However, the field is still far from achieving the dynamic range expected from the proteome, so expect many more generations and novel platforms from your favorite vendors.

What do you think we can do to encourage interdisciplinary interactions between mass spectrometrists and cardiovascular researchers?

The solution is easy to state but not so easy to implement. Institutes need to look at CICS as an example. Department chiefs, directors or chairs need to invest the time and resources to bring on board the expertise and technology. In my opinion, every research department should have one proteomics/mass spectrometry group, and a program that fosters close collaborations between the mass spectrometry lab and the other groups in the department. I have spoken to many innovative cardiovascular scientists that have great desires to collaborate with a proteomics group, but cannot find a match because there are too few labs to help everyone. When a match is made, even collaborations between departments can be challenging, much less between institutions.

So researchers and faculty that have influence on the design and future of their department should push to include a mass spectrometry program.

If you could solve one research problem, what would it be?

I wish we could monitor the movement of any protein or all proteins in a live cell. Our research would be greatly facilitated if we could just see what our favorite protein is doing in real time. We would rely less on indirect methods to know its localization, binding partners and half-life. Indirect methods always introduce artifacts that lead us astray in research. With a little bit of imagination I think I have a solution, but I’m sure the IPS, genome editing and synthetic biology folks are already working on it.

Will a Canadian team ever again hoist Lord Stanley’s Cup?

Yes, in an all Canadian Cup final that could also include the Buffalo Sabres. (Editor’s note: Is this the first part of a Canadian plot to invade upstate New York?)

Any final thoughts?

Yes, mass spectrometry is here to stay, so let’s keep talking about it.

Be sure to catch Sasha Singh’s lecture as part of our next installment of the ISACB Webinar Series! More information here: http://isacb.org/webinars